In theory, I should be able to set and export PERL5LIB in the root shell before starting Apache2 and have the contents added to %INC.

Your use of "the root shell" instead of "a root shell" is making me think you ran a shell as root, set some environment variable, and figured it would be available to all processes running as root. It will only be available to children of that shell process.

Either way, I'm certain that mod_perl can be configured in this respect via the Apache config files.